[Bioperl-l] is the Bio::Align::AlignI doc right?

[Chris Fields]

Yes, but this has been long corrected on main trunk and the latest CPAN code (1.6.1).  v.1.2.3 is very old, very very very old.  Dinosaurs and perl 5.6.1-old.  You should update, even if you are using ensembl's perl API ;>

chris

On Feb 25, 2010, at 6:35 AM, Ben Bimber wrote:

> below is a Bio::Align::AlignI example found here:
> 
> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Align/AlignI.pm#column_from_residue_number
> 
> 
> Title   : column_from_residue_number
> Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
> Function:
> 
>           This function gives the position in the alignment
>           (i.e. column number) of the given residue number in the
>           sequence with the given name. For example, for the
>           alignment
> 
>             Seq1/91-97 AC..DEF.GH
>             Seq2/24-30 ACGG.RTY..
>             Seq3/43-51 AC.DDEFGHI
> 
>           column_from_residue_number( "Seq1", 94 ) returns 5.
>           column_from_residue_number( "Seq2", 25 ) returns 2.
>           column_from_residue_number( "Seq3", 50 ) returns 9.
> 
> 
> Perhaps I am simply misunderstanding the method, but shouldnt the first
> example return 6, not 5?
> 
> E is the 94th residue.  It is in the 6th column.  Am I missing something?
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